[FEATURE REQUEST] Add "function" column to anvi-compute-functional-enrichment-across-genomes output

[kellikmullane]

The need

I'm not sure if this used to be a function and it got lost/dropped at some point (or hopefully it's not just an issue with my machine/install), but I've been using anvi-compute-functional-enrichment-across-genomes a ton, and have found it tedious and time-consuming (especially with the number of genomes/groups I'm working with) to analyze the output in a meaningful way. While the functional-enrichment.txt output provides an accession value, it does not list the actual function associated with the accession.

What I've been having to do is either look up the accession online, or cross-reference it with the functional occurrence table (provided by the additional parameter --functional-occurrence-table-output). While this is fine, it would save SO much time if this "function" was just included in the functional-enrichment.txt output.

I saw on the Microbial Pangenomics Tutorial that the output shown under the "Quantifying functional enrichment in a pangenome" section does list the function in the output, but this example uses anvi-compute-functional-enrichment-in-pan.

The solution

Add a "function" column in the functional-enrichment.txt output of anvi-compute-functional-enrichment-across-genomes.

Beneficiaries

I think this would be of great benefit to anyone who uses the command anvi-compute-functional-enrichment-across-genomes.

[meren]

Hey @kellikmullane, thank you very much for reporting this. I'm not sure what happened, but we indeed lost that column at some point :) I just fixed the problem in the codebase. Please git pull your anvio-dev and try again. You should find the functional annotation column in your updated output file.

Best wishes,

[kellikmullane]

Ohh wow - thanks for getting to this so quickly! You have no idea how much time this will save me - thank you!!